11-126293229-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000392678.7(TIRAP):c.*112C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 1,232,986 control chromosomes in the GnomAD database, including 377,721 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.73 ( 41951 hom., cov: 32)
Exomes 𝑓: 0.79 ( 335770 hom. )
Consequence
TIRAP
ENST00000392678.7 3_prime_UTR
ENST00000392678.7 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.42
Genes affected
TIRAP (HGNC:17192): (TIR domain containing adaptor protein) The innate immune system recognizes microbial pathogens through Toll-like receptors (TLRs), which identify pathogen-associated molecular patterns. Different TLRs recognize different pathogen-associated molecular patterns and all TLRs have a Toll-interleukin 1 receptor (TIR) domain, which is responsible for signal transduction. The protein encoded by this gene is a TIR adaptor protein involved in the TLR4 signaling pathway of the immune system. It activates NF-kappa-B, MAPK1, MAPK3 and JNK, which then results in cytokine secretion and the inflammatory response. Alternative splicing of this gene results in several transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 11-126293229-C-T is Benign according to our data. Variant chr11-126293229-C-T is described in ClinVar as [Benign]. Clinvar id is 2688397.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TIRAP | NM_001318777.2 | c.646+174C>T | intron_variant | ENST00000392679.6 | NP_001305706.1 | |||
TIRAP | NM_001039661.2 | c.646+174C>T | intron_variant | NP_001034750.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.733 AC: 111400AN: 151928Hom.: 41915 Cov.: 32
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GnomAD4 exome AF: 0.786 AC: 849810AN: 1080940Hom.: 335770 Cov.: 14 AF XY: 0.790 AC XY: 430528AN XY: 544930
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GnomAD4 genome AF: 0.733 AC: 111489AN: 152046Hom.: 41951 Cov.: 32 AF XY: 0.743 AC XY: 55227AN XY: 74304
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 58% of patients studied by a panel of primary immunodeficiencies. Number of patients: 51. Only high quality variants are reported. - |
Computational scores
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CADD
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DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at